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microRNAs reveal the interrelationships of hagﬁsh,lampreys,and gnathostomes and the nature ofthe ancestral vertebrateAlysha M.Heimberga,Richard Cowper-Sal∙larib,Marie Sémonc,Philip C.J.Donoghued,1,and Kevin J.Petersona,1aDepartment of Biological Sciences,Dartmouth College,Hanover,NH 03755;bDepartment of Genetics,Dartmouth Medical School,Hanover,NH 03755;cInstitut de Génomique Fonctionnelle de Lyon,Université de Lyon,Centre National de la Recherche Scientiﬁque,Institut National de la RechercheAgronomique,Ecole Normale Supérieure de Lyon,69364 Lyon Cedex 07,France;anddDepartment of Earth Sciences,University of Bristol,Bristol BS8 1RJ,United KingdomEdited* by J.William Schopf,University of California,Los Angeles,CA,and approved September 22,2010 (received for review July 15,2010)Hagﬁsh and lampreys are the only living representatives of thejawless vertebrates (agnathans),and compared with jawed verte-brates (gnathostomes),they provide insight into the embryology,genomics,and body plan of the ancestral vertebrate.However,thisinsight has been obscured by controversy over their interrelation-ships.Morphological cladistic analyses have identiﬁed lampreysand gnathostomes as closest relatives,whereas molecular phylo-genetic studies recover a monophyletic Cyclostomata (hagﬁsh andlampreys as closest relatives).Here,we show through deepsequencing of small RNA libraries,coupled with genomic surveys,that Cyclostomata is monophyletic:hagﬁsh and lampreys share 4unique microRNAfamilies,15 unique paralogues of more primitivemicroRNAfamilies,and 22 unique substitutions to the mature geneproducts.Reanalysis of morphological data reveals that supportfor cyclostome paraphyly was based largely on incorrect charac-ter coding,and a revised dataset is not decisive on the mono- vs.paraphyly of cyclostomes.Furthermore,we show fundamentalconservation of microRNA expression patterns among lamprey,hagﬁsh,and gnathostome organs,implying that the role of micro-RNAs within speciﬁc organs is coincident with their appearancewithin the genome and is conserved through time.Together,thesedata support the monophyly of cyclostomes and suggest that thelast common ancestor of all living vertebrates was a more complexorganism than conventionally accepted by comparative morphol-ogists and developmental biologists.complexity|cyclostomata|evolution|organ|homologyThe origin and early evolution of vertebrates have been a focusof molecular and organismal evolutionary biology because ofthe fundamental events that attended this formative episode ofour own evolutionary history over one-half billion years ago (1).However,attempts to integrate these perspectives have beenstymied by the different phylogenetic perspectives afforded bymolecular and morphological datasets.Molecular datasets,in-corporating protein-coding genes,ribosomal RNA genes,and/ormitochondrial genes (2–21),invariablyﬁnd that the jawless hag-ﬁsh and lampreys constitute a clade,Cyclostomata (Fig.1,on theleft).In contrast,morphological datasets (22–36) have supporteda closer relationship between lampreys and gnathostomes,ren-dering Cyclostomata paraphyletic (Fig.1,on the right) and hag-ﬁsh not vertebrates but mere craniates (33).Attempts have been made to reconcile these two views:a num-ber of morphological characters have been identiﬁed that supportthe monophyly of cyclostomes (37,38),but they have been over-whelmed by a seemingly far greater number of characters sup-porting cyclostome paraphyly (30,31).Indeed,an analysis ofcombined morphological and molecular datasets has suggestedthat the signal of cyclostome paraphyly in morphological datasetsis stronger than the signal for monophyly from molecular data(39).The interrelationships of hagﬁsh,lampreys,and gnathos-tomes thus remain uncertain,and this has become a classic ex-ample of phylogenetic conﬂict between morphological and mo-lecular data (7,39).If morphological phylogenies are correct,hagﬁsh provide an experimental model for investigating the evo-lutionary assembly of the vertebrate body plan shared by lampreysand gnathostomes.Alternatively,if the molecular phylogeniesare correct,then it would indicate that the shared similarities oflampreys and gnathostomes are convergent or that these charac-ters are absent through loss in the hagﬁsh lineage.These wouldrepresent the most extraordinary examples of convergence or de-generacy,respectively,in vertebrate evolutionary history (18,35).We attempted to resolve the interrelationships of hagﬁsh,lampreys,and gnathostomes through analysis of their microRNA(miRNA) repertoire.miRNAs are small,noncoding regulatorygenes implicated in the control of cellular differentiation and ho-meostasis and as such,might be involved in the evolution of com-plexity (40–42).Because ancient miRNAs showa level of sequenceconservationexceeding that of ribosomal DNA(43),it is possible todiscern the evolutionary origins of miRNA families at even thedeepest levels of animal phylogeny (43,44).The rarity with whichancient miRNAs were lost within most evolutionary lineages,coupled with the continuous acquisition of miRNAs through geo-logic time in all metazoan lineages examined to date,makesmiRNAs one of the most useful classes of characters in phyloge-netics (45).Thus,miRNAs can be used to discern the interrela-tionships among the major vertebrate lineages and simultaneously,lend insight into the origin of vertebrate characteristics.We constructed small RNA libraries from total RNA (Meth-ods) from ammocoete larvae of the brook lampreyLampetraplaneri,from a single adult individual of the Atlantic hagﬁshMyxine glutinosa,fromthe catsharkScyliorhinus canicula,and fornine individually processed organs/regions (brain,gills,gut,heart,kidney,liver,mouth,muscle,and skin) from a single adultindividual of the sea lampreyPetromyzon marinus.Using a com-bination of high-throughput 454 pyrosequencing and Illuminatechnology,we identiﬁed miRNAs from each library and foundthat shared gains of miRNAs support the monophyly of cyclo-stomes (lamprey and hagﬁsh).We also revised,expanded,andreanalyzed an extensive morphological dataset previously foundto support cyclostome paraphyly (23) and show that cyclostomeAuthor contributions:A.M.H.,P.C.J.D.,and K.J.P.designed research;A.M.H.,P.C.J.D.,and K.J.P.performed research;R.C.-S.and M.S.contributed new reagents/analytic tools;A.M.H.,P.C.J.D.,and K.J.P.analyzed data;and A.M.H.,P.C.J.D.,and K.J.P.wrote the paper.The authors declare no conﬂict of interest.*This Direct Submission article had a prearranged editor.Data deposition:The data reported in this paper have been deposited in miRBase,www.mirbase.org.See Commentary on page 19137.1To whom correspondence may be addressed.E-mail:phil.donoghue@bristol.ac.uk orkevin.j.peterson@dartmouth.edu.This article contains supporting information online atwww.pnas.org/lookup/suppl/doi:10.1073/pnas.1010350107/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1010350107 PNAS|November 9,2010|vol.107|no.45|19379–19383EVOLUTIONSEECOMMENTARYmonophyly is just as likely given these data.In addition,proﬁlingthe miRNA expression within nine organs ofP.marinusshowsconservation with known expression proﬁles in homologousorgans across vertebrates.Our data suggest that the role ofmiRNAs within speciﬁc organs is coincident with their appear-ance within the genome,and thus,miRNAs may have playeda role in the acquisition of organismal complexity in vertebrates.Results and DiscussionmiRNAs Shared Between Lampreys and Hagﬁsh Support CyclostomeMonophyly.Derivative cDNA libraries from the brook lampreyL.planeri,the sea lampreyP.marinus,and the Atlantic hagﬁshM.glutinosawere sequenced using high-throughput 454 pyrose-quencing (Methods),yielding 422,122 (59,759 nonredundant)parsed high-quality reads.Additionally,we sequenced smallRNAs fromthe catsharkScyliorhinus caniculausing Illumina tech-nology,yielding 333,294 (127,015 nonredundant) parsed high-quality reads.The resulting reads from all four taxa were theninterrogated using miRMiner (43) to identify known and unknownmiRNAs (Dataset S1).Because the genome traces of the sea lampreyP.marinusarepublicly available (http://www.ncbi.nlm.nih.gov/genomeprj?term=petromyzon),weﬁrst focused on elucidating the miRNA reper-toireof this species.Weidentiﬁed245miRNAgenes inP.marinus,including one family lost in gnathostomes (miR-315) and a secondfamily lost in osteichthyans (mir-281) (Dataset S1).An additional24 miRNA genes are inferred to be present in the genome ofP.marinus,because,althoughthe genes couldnot be locatedinthetrace archives,reads of these phylogenetically conserved miRNAswere discovered in our libraries (e.g.,miR-31,-34,-122,etc.)(Dataset S1).Of the 269 genes present inP.marinus,202 areconserved in other animals,with 21 shared only with the brooklamprey,L.planeri(Dataset S1).Lampreys lack the bilaterian miRNAs miR-71,miR-242,miR-252,and miR-278,as do urochordates and all other vertebratesexamined to date.However,very few miRNA genes have beenlost within the lamprey lineage itself:only a single miRNAfamilyseems to have been lost inP.marinus(miR-214),because readswere detected inL.planeri(Dataset S1);however,reads werenot detected inP.marinus,and the gene was not located in thetrace archives.Conversely,we failed to detect transcripts of onlytwo miRNA families inL.planeri—the lowly expressed miRNAs(Dataset S1) miR-202 and miR-875 (although we did not ex-amine reads from an adult individual,and no genomic sequencefor this species is currently available to conﬁrm a true absence).Therefore,these two lamprey species share a miRNA comple-ment of at least 200 genes and between them,have together lostno more than three miRNA families total since they last shareda common ancestor some time in the last 10–40 million y (10).To determine the phylogenetic position of hagﬁsh,we ana-lyzed the conserved miRNA complement ofM.glutinosa.Of the46 vertebrate-speciﬁc miRNA families shared between lampreyand gnathostomes (Fig.2),we detected all but two in our hagﬁshlibrary:miR-1329 (which is expressed exclusively in the lampreykidney) (Dataset S1) and miR-4541,an miRNAfamily found thusfar only in the two sharks and the two lamprey species (DatasetS1).However,the hagﬁsh shares four unique miRNA familieswith the lampreys that are not found or expressed in gnathos-tomes or in any other animal species investigated to date,miR-4542,miR-4543,miR-4544,and miR-4545 (Dataset S1andFig.S1),and a phylogenetic analysis based on the presence and ab-sence of miRNAfamilies (Dataset S2) supports the monophyly ofthe cyclostomes (Fig.2 andFig.S2).Further evidence of cyclostome monophyly is found in theparalogy group relations within miRNA families (46).Fifteenparalogues of previously described miRNA families (Fig.3 andDataset S1) are shared by the hagﬁsh and lampreys to the ex-clusion of gnathostomes—we did not detect a single paraloguesupporting cyclostome paraphyly.Finally,we examined the ma-ture sequences of each miRNA to ask if polarizable nucleotidesubstitutions had occurred that supported either cyclostomemonophyly or paraphyly (or some other set of relations).We didnotﬁnd any nucleotide substitutions in the mature sequence ofany vertebrate miRNA that is shared between gnathostomes andlampreys to the exclusion of hagﬁsh (or between hagﬁsh andgnathostomes to the exclusion of lamprey).However,we didﬁnd22 derived nucleotide substitutions in the mature sequences of18 miRNAs exclusive to the three cyclostome taxa investigated(Fig.3 andDataset S1).Thus,the acquisition of miRNA fami-lies,miRNA genes,and the nucleotide substitution patterns ofconserved miRNA genes all support cyclostome monophyly.Phenotypic Cladistic Data Do Not Distinguish Between CyclostomeMonophyly vs.Paraphyly.The phylogenetic distribution of verte-brate miRNAs corroborates molecular sequence data in sup-porting cyclostome monophyly (2–21),contradicting what hasbeenconsidered anequally strong signal fromphenotypic datasetssupporting cyclostome paraphyly (22–36).To determine thesource of this discordance,we augmented a phenotypic datasetbased on the nervous system (23),with characters representativeof other organ systems recoded from observations and the pri-mary literature rather than recycled from previous analyses (SITextandDataset S3).In so doing,we considered all charactersthat have been marshaled previously in support of cyclostomemonophyly or paraphyly.Weﬁnd that,although the reviseddataset (SI Text) marginally favors cyclostome paraphyly (mono-phyly is one step longer in a tree of 237 steps) (Fig.S3),Tem-pleton (47),Kishino–Hasegawa (48),and approximate two-tailedShimodaira–Hasegawa (49) tests reveal that the dataset isindecisive on this question (Templeton:P= 0.8415;K–H:P =0.8421;approximate S–H is one-halfPof K–H) (49).This is be-cause much of the evidence traditionally interpreted as supportingcyclostome paraphyly has been based on spurious character de-sign.For example,many of the characters are inapplicable to theoutgroup,making it impossible to discriminate between the pri-mary or secondary absence in hagﬁsh of characters otherwisefound only in lampreys and gnathostomes (e.g.,the proximity ofthe atrium and ventricle of the heart,radial muscles,and retinalsynaptic ribbons).In addition,some characters have been codedas absent in hagﬁsh when data have merely been lacking (e.g.,heart response to catecholamines,pituitary control of gameto-genesis,and sexual dimorphism).Finally,the uncritical recyclingof characters and their codings between generations of analyseshas resulted in the repeated use of obsolete data (50).For in-stance,similarities in the immune system of lampreys and gna-thostomes have been exploited to draw a distinction fromhagﬁsh(30–35,51).However,it has been long established that lampreysFig.1.The two competing hypotheses.Either lampreys are more closely re-lated to hagﬁsh than they are to gnathostomes,making Cyclostomata mono-phyletic (on the left),or lampreys are more closely related to gnathostomesthan they are to hagﬁsh,making Cyclostomata paraphyletic (on the right).19380|www.pnas.org/cgi/doi/10.1073/pnas.1010350107Heimberg et al.and hagﬁsh share a distinct type of adaptive immune systembasedon variable lymphocyte receptors,rather than the Ig-based T andB antigen receptors that characterize the lymphocytes of jawedvertebrates (52),and thus,similarities in the immune system oflampreys and jawed vertebrates are convergent.miRNA Expression Proﬁles Are Conserved Across Vertebrates.Theorigin of vertebrates occurred in association with a very highrate of miRNA family innovation,and it has been proposed thatthis is a causal association,because where expression data areavailable,vertebrate miRNAs are often expressed in tissues andorgans that are unique to vertebrates (41).This hypothesis pre-dicts that the organ-speciﬁc expression of vertebrate-speciﬁcmiRNAs is highly conserved,such that data from the zebraﬁsh(Danio) and the mouse (Mus) are representative not only ofosteichthyans (the clade that they circumscribe) but of vertebratesmore generally.Our phylogenetic results indicate that a compar-ison of existing data with lampreys will provide an adequate testof the hypothesis,because together,these taxa circumscribe theclade of all living vertebrates (Fig.2).Expression data for sevendifferentP.marinusorgans are shown in Fig.4.Similar toDanio(53,54) andMus(55),each lamprey organ expresses a speciﬁcsuite of miRNAs that gives the organ a unique miRNAexpressionproﬁle.For example,ignoring the ubiquitously expressed let-7,the four highest expressed miRNAgenes in the lamprey brain aremiR-9a,miR-338a,miR-138a,and miR-125a,whereas the fourhighest expressed miRNAgenes in the lamprey gut are miR-194,miR-192,miR-200a,and miR-429 (Fig.4 andDataset S4).Fur-thermore,similar to mouse (56),the lamprey brain is the mostcomplex of the organs queried,and the gut and liver are the least,at least in terms of the number of different miRNAs expressed(Dataset S4).With just one exception (the heart),the miRNAwith the highest expression in each of the lamprey organs is alsoexpressed in that same organ in bothDanio(Fig.4Insets) andhagﬁsh (Fig.S4).Thus,homologous organs in vertebrates moreoften than not (57) express homologous miRNAs,consistent withthe hypothesis that miRNAs (e.g.,miR-30 and miR-122) wereinstrumental in the evolutionary origin of vertebrate-speciﬁcorgans (e.g.,kidney and liver,respectively) (41).ConclusionsHinging on debate over the interrelationships of living jawlessand jawed vertebrates has been the nature of the ancestral ver-tebrate and the pattern and sequence of organismal and genomicevolution,on which hypotheses of developmental evolution arebased.We conclude that cyclostomes are monophyletic,and thus,characters reconstructed as lamprey and gnathostome synapo-morphies are actually shared primitive characters of all verte-brates,with hagﬁsh anatomy having degenerated to a remarkabledegree (18,36).Cyclostome paraphyly (22) and a hierarchicaldistinction between craniates and vertebrates (33) afforded in-sight into the assembly of vertebrate characters (58).With therecognition of cyclostome monophyly,however,that taxonomicdistinction and evolutionary insight are lost.Evidently,the crownancestor of vertebrates was more complex,phenotypically andFig.2.Phylogenetic distribution of all miRNA families analyzed in chordates (seeDataset S2for data matrix andFig.S2for complete phylogenetic analysis).Cyclostomes share four miRNA families not found in any other animal species investigated to date,and a maximum parsimony analysis supports themonophyly of Cyclostomata.Note that miRNA families speciﬁc to a single species are not indicated,but losses of more primitive families are indicated.Ofparticular interest is the number of miRNA families acquired in the stem lineage leading to the vertebrate crown group.Fig.3.The presence of paralogues of more primitive miRNA families andconserved nucleotide substitutions both support the monophyly of Cyclo-stomata.Shown is miR-19 as an example of a group of miRNAs that showsboth conserved nucleotide substitutions (19a;Top,bold) with respect to theother paralogue(s) (19b and 19c;MiddleandBottom) and the possession ofa paralogue (miR-19c) not present in any known gnathostome (Dataset S1has the complete description of both paralogues and nucleotide sub-stitutions supporting cyclostome monophyly).Cmi,Callorhinchus milii;Dre,Danio rerio;Hsa,Homo sapiens;Lpl,Lampetra planeri;Mgl,Myxine gluti-nosa;Pma,Petromyzon marinus.Heimberg et al.PNAS|November 9,2010|vol.107|no.45|19381EVOLUTIONSEECOMMENTARYdevelopmentally,than has been perceived hitherto (58),makingattempts to explain mechanistically the distinction between ver-tebrates and invertebrates even more formidable.Nonetheless,inreconciling phylogenies grounded in genotype and phenotype,weprovide a holistic framework for uncovering the formative eventsin the evolutionary emergence of vertebrates.We predict that therenaissance in hagﬁsh embryology (59) will further show the lossof vertebrate characters,but with the recognition of cyclostomemonophyly,attempts to dissect the assembly of the vertebratebody plan can be focused on comparative analysis of lampreydevelopment and genomics.The proliﬁc origin of miRNA fami-lies in the vertebrate stem-lineage and their expression in verte-brate-speciﬁc tissues and organs supports the idea that miRNAsplayed a pivotal role,as part of a broader gene regulatory land-scape,in the assembly of the vertebrate body plan (41).MethodsTotal RNA Extraction,Northern Analysis,and Small RNA Library Construction.Embryonic brook lampreys (L.planeri)were collected from Highland Water,upstream of Millyford Bridge,New Forest National Park (United Kingdom)and allowed to develop in captivity at 16 °C inﬁltered river water untilhatching.Adult sea lamprey (P.marinus) were collected from Lake Cham-plain (Vermont),and a single individual was dissected to isolate the brain,gut,gills,heart,kidney,liver,mouth and tongue,muscle,and skin.Atlantichagﬁsh (M.glutinosa)were collected at Kristineberg Marine Station,Gul-marsfjord,Sweden and purchased from Gulf of Maine Inc.(Pembroke,ME).RNA was extracted from 20 combined larvalL.planeri,from each dissectedtissue and organ derived from a single adultP.marinus,and from a singleadultM.glutinosa.Fromthese animals,small RNA libraries were constructedindividually and sequenced with a unique barcode using 454 DNA pyrose-quencing (Branford,CT) as described previously (43).The resulting reads werethen analyzed with miRMiner to identify known and unknown miRNAs (43),with additionalﬁlters for transfer and ribosomal RNAs written with customshell scripts.RNAwas also extracted fromthe brain,gut,heart,kidney,liver,muscle,andskin derived from a single adultM.glutinosa,and northern analyses usingStarﬁre probes (IDT) designed against the mature miRNA sequence (sequencesavailable on request) were performed as previously described (43).Catshark(S.canicula) embryos were obtained from commercial sources,and RNA wasextracted fromﬁve embryos near hatching.S.caniculaRNA was sequencedFig.4.miRNA expression proﬁle of seven different lamprey organs.Only the top 10 highest expressed miRNAs (Dataset S4) are shown,and each speciﬁcmiRNA is given a distinct color for all pie charts.Below each pie chart is the expression pattern of the highest expressed gene in the lamprey library inthezebraﬁsh (54)—note the concordance between the lamprey and zebraﬁsh for all organs queried except for the heart (Bottom).Pma,Petromyzon marinus;Dre,Danio rerio;Mmu,Mus musculus.19382|www.pnas.org/cgi/doi/10.1073/pnas.1010350107Heimberg et al.for small RNAs using the Illumina sequencing platform and analyzed usingmiRMiner as described (43).All genomic inquiries for miRNAs inP.marinusandCallorhinchus milii(elephant shark) were made through National Center forBiotechnology Information using the available genomic traces.All alignmentsand sequence analyses were performedusing MacVector (v.10.0.2).Secondarystructures of precursor miRNA transcripts were predicted using mFold (60).Morphological Analysis.The phenotypic dataset was coded directly from theprimary literature and from direct observation of anatomy (SI Text).Wedesigned and coded characters using a contingent coding strategy,because itis the only approach that is theoretically and operationally valid in instances,as here,where many of the characters are inapplicable to the outgroup (61).We restricted our analyses to a parsimony-based approach,because pheno-typic support for hagﬁsh–lamprey–gnathostome relationships has alwaysbeen debated using this method of phylogenetic inference.The cladisticparsimony analyses,Bremer support index calculations,and Templeton andKishino–Hasegawa tests were performed in PAUP*4.0b10 running on MacOS9 within a Sheepshaver 2.3 emulator on an Intel MacBook.ACKNOWLEDGMENTS.We thank E.Marsden,S.Shimeld,and M.Thorndykefor access to materials and J.Mallatt,E.Sperling,D.Pisani,and M.Schubert forcomments on a previous draft.P.C.J.D.is supported by the Biotechnology andBiological Sciences Research Council,European Commission Seventh Frame-work Programme EU FP7,The Leverhulme Trust,Natural Environment Re-search Council,and National Endowment for Science Technology and theArts (NESTA);K.J.P.is supported by the National Aeronautics and Space Ad-ministration/Ames and National Science Foundation.A.M.H.was supported byAward Number T32GM008704 fromthe National Institute of General MedicalSciences of the National Institutes of Health.1.Shimeld SM,Holland PWH (2000) Vertebrate innovations.Proc Natl Acad Sci USA97:4449–4452.2.Stock DW,Whitt GS (1992) Evidence from18S ribosomal RNAsequences that lampreysand hagﬁshes form a natural group.Science257:787–789.3.Delsuc F,Tsagkogeorga G,Lartillot N,Philippe H (2008) Additional molecular supportfor the new chordate 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